This project is concerned with the molecular epidemiology of cancer, beginning with the realization that as many as half a dozen independent genetic and epigenetic events may be involved in the transformation from a normal cell to malignancy. The changes in genomic DNA occur at specific sites and can lead to activation of protooncogenes or inactivation of tumor suppressor genes through mutation, recombination, gene amplification, translocation, or other chromosomal abnormalities. In some human hereditary diseases an increased incidence of neoplasia is correlated with a defect in the repair and/or replication of damaged DNA. Our ultimate objective is to understand how the processing of damaged DNA in mammalian cells relates to carcinogenesis. Having pioneered in the development of sensitive techniques for quantifying particular DNA lesions in restriction fragments from specific regions of the genome we will extend our analysis of intragenomic fine structure of DNA repair, to learn the factors that control the efficiency of the process in chromatin and in different functional domains of the genome, such as replication origins and expressed genes transcribed by different RNA polymerases. Having discovered preferential repair of the transcribed DNA strand in expressed genes, we will test a model for transcription-coupled repair based upon factors that enhance transcript shortening by the 5'- 3' exonuclease activity of RNA polymerase II. We will critically test the possibility that strand-specific DNA repair can be used as a sensitive assay for transcription. Nuclear matrix associated DNA will be characterized to determine whether that is the site of transcription-coupled repair. Domain limited repair in xeroderma pigmentosum, complementation group C, will be assessed to learn the basis for the cancer prone phenotype, and the deficiency in repair of expressed genes in Cockayne's syndrome will be studied to understand the basis for the defect and the absence of cancer proneness. Differences in the repair of particular genes at risk may account for some of the profound differences seen in the carcinogenic responses of different tissues and of the same tissue in different organisms. Plasmid probes carrying lesions at defined sites will be used in the analysis of specific sequence repair in cells of different genetic background. The defined chimeric plasmids will also be used to introduce genes into different genomic domains to study the specific features of damage processing that result in the enhanced integration of damaged DNA in human cells. We will also explore the possible role of localized DNA turnover in non-proliferating cells in the fine structure of mutagenesis to test our hypothesis that transcription- associated DNA turnover may result in anomalous high mutation frequencies in some domains. This research should contribute substantially to our understanding of the basis for DNA damage processing deficiencies in certain cancer-prone hereditary diseases and it should also result in new, sensitive probes for the analysis of damage and repair in human cells. In addition, our studies should help to interpret the role of DNA damage and DNA turnover in biological end points such as survival, mutagenesis, and carcinogenesis.